Archive for September, 2009

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Where am I?

September 27, 2009

Yesterday, as part of our “orientation”/ department sponsored social events, a small group of us went hiking at a nearby state park. Although poorly attended by my fellow classmates (which is hypocritical for me to say because I almost didn’t go…) the trip was definitely highly anticipated and definitely worth it.

I love to hike. I never really got to do it a whole lot in undergrad as a result of being extremely busy with school and living so close to a major metropolitan area (it’s hard to convince your friends to drive an hour and a half away to go hiking when the big city is a 30 minute el ride away).

But getting away to nature is definitely a favorite past time. There’s something about being in it, being surrounded by life, surrounded by freshness, surrounded by old trees, that really puts things together. Life makes sense in the chaos of the forest.

As I sit in the cold confines of my laboratory bench and chair, reading about the godlessness of the universe when I should be reading about the homology, or sameness, between yeast and humans, I wonder what the heck I’m doing. Is this gel that I just accidentally set on fire because I misread the voltmeter going to get me closer to understanding? Is this book about the inanities of religion getting me farther from god? Or do I just need to go for a walk, and let my mind wander the light peaking through the trees, the scent and musk of the flowers and animals, the babble of the brook and the crackle of the creek?

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Networks

September 14, 2009

Sorry for the lack of updates. It’s a busy time.

But I’m going to post this pretty awesome article theorizing how social networks play a role in our health and happiness. The idea of networks is something I’ve always wanted to study more (the sociologist in me). How one person can affect their friends and strangers, how the type-A personality can start a revolution, how ideas and open-mindedness can lead to progressive change, etc.

The statistical work they do is a little on the sketchy side, and the source of data, though large, needs to be a little more comprehensive. But all in all, a good, long read.


Here’s the article

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Lateral Meme Transfer

September 6, 2009

So the first paper I had to read in my Cell Bio course was a paper by Carl Woese at the University of Illinois from 1998 called “The universal ancestor.” LUCA, or Last Universal Common Ancestor by many scientist, is our sort of Adam and Eve: some simple cell from which environmental factors and genetic mutations led to the vast array of organisms we see and observe today, including ourselves. His theory, in short, is that LUCA could not have been one species as we know it today, having all of the essential little biological processes we see in our cells or even simpler organisms like bacteria. Instead he proposes that LUCA was instead a community of “progenotes” or extremely simple cells that lack large RNA sequences with each cell providing a different crucial aspect to life. As the community of cells survived, they had to give and share with each other, proving that the cells were not self sufficient as we would see later.

In the paper he says that the method of evolution for LUCA was different than the method we see today. Today we evolve through genetic inheritance. Family trees. Mom and Dad are different from each other, they have a kid, and if that kid got good aspect of mom and good aspect of dad, he will survive to adulthood and produce a bunch of children who hopefully will also have those same good aspects. Aspects in this case being genes that lead to a stronger ability to survive. But in the chaotic … cluster fuck … of the progenotes, everything evolved differently. Calling it lateral gene transfer, he proposes that the cells of LUCA easily shared genetic information. If things worked well the genetic information could move around and be taken by other cells and if things failed, the information would be quickly lost as those cells died. So evolution moved extremely fast with direct genetic movement from cell to cell instead of what we have today that requires slow generational movement.

An interesting aspect of his paper is his discussion on translation. Translation is how genetic information, like RNA and DNA, become proteins, proteins being the workers of the cell. He says the poor early ribosomes, ribosomes being the RNA machinery that does translation, were extremely inefficient. This means that mutation rates were high, and only small proteins could be made from equally small genomes. And with eventual efficient ribosomes being made that had much better accuracy, traditional vertical, family tree inheritance could occur. Because with better ribosomes meant less mutation and larger proteins which could not be genetically transferred laterally. This all just reminded me of HIV. HIV relies on a poorly functioning reverse transcriptase to be able to adapt to anything. But this is a side note and I’ll get back on topic…

While this theory of his is based on supposition, although his reasoning is extremely well thought out and very believable, the idea of lateral inheritance is an important one. I’ve been thinking about religion a lot lately. Being around the nonbelievers (aka, the biologists) have really got me thinking. Biologists tend to, more than any other science, reject religion. This is the result of evolution being a major aspect of our career. “Nothing in biology makes sense except in the light of evolution” a famous quote by Theodosius Dobzhansky. We stake our experiments on evolution. I’m currently working on a project in yeast that looks at a system in yeast that is conserved in humans. Without evolution, I’m wasting my time: who cares about yeast. But with evolution, I’m looking at a system so important to life, even a single celled organism has it.

But is rejecting religion a bad thing?

I’m going to make the case, with lateral gene transfer, that it might be. This is coming from a biologist, remember. A godless biologist at that.

Religion is a very important aspect of our development into society. Religion brings our people together and gives us a culture. For I don’t know how long, religion has worked in doing that. Look at marriage. A religious institution, it has for the longest time, brought two people together to care and nurture their children. What is more evolutionarily stronger than this institution? We have a long tradition of courtship that leads to two dissimilar people (opposites attract) getting together and sharing their differing genes. Then we bind them together to ensure that these children survive the difficulties of childhood and become successful, child bearing adults. Marriage is a meme that proved to succeed in raising tons of strong children, so it stuck.

(Skip this is you know about memetics) A meme is a cultural gene. The theory of memetics is relatively new (1970’s Selfish Gene by Richard Dawkins). It states that we pass down genes to our children. But with human thought, we have developed a new self replicating “gene” that strictly relates to culture. He called these meme’s, or the cultural genes that like genes, go through evolution and natural selection. Some memes survive, marriage, and some die, Pogs. And some memes evolve, in this case religion.

So religion is, in my opinion, the most successful meme(s). It has held so many societies together, keeping children alive, and getting us to work together and live longer. It keeps us moral, defining what is good, like helping out your neighbors, and bad, killing your neighbors. It has led to cultural bloom: JS Bach is considered one of the best composers, and his Mass in B minor is considered one of the best works ever written, and it’s church music!

But only recently have we seen a different ideology spread. With mass communication and an acceptance of free thought, we are seeing it possible to be moral, care for children, form a working society without religion. Atheism is spreading, and not resulting in tons of anarchists burning houses down and lynching Christians. So is this the end of religion? Maybe.

But I doubt it. Because as ironic as it is, religion, specifically Christian religion, has child bearing in it’s roots. The Duggars have 19 kids with more on the way. Not because pregnancy is some kinky infatuation, but because God told them children are gifts from up above, so more gifts are better than less. But that’s evolution! The person with the most successful progeny wins! And ironically, the godless people working in media are providing them with money to show godless America a crazy Christian household. Guess what, the godless are giving this Christian family money to be even more successful, both evolutionarily and societally.

But are the atheists producing 19 children? Are we listening to the word of Darwin and crapping out as many children as we can to spread our thinking in the world. And I have a feeling we’re not. Even Richard Dawkins, who many biologists have come to view as the atheistic leader of evolutionary thought, has only one child. That guy should be producing tons of children to someday spread his thought to the world. He preaches a militant atheism. How does he plan to do it without vertical, family tree inheritance of ideas?

He does it by lateral meme transfer. If atheists aren’t having enough kids to pass this ideology down, they need to spread it laterally. Show the rising youth, confused by war and famine in spite of one dollar spicy chicken sandwiches at BK, a scientific view of life. Show them that hoping for a peaceful, paradise heaven is affecting their happiness in the life they are experiencing today. Show them that they too can have a family, a marriage, and a happy, successful life, without god.

Atheism depends on lateral conversion. So many families are ingrained into their religious ways, and with atheist families so small in number, the only way to make is to convert them.

Will it succeed? I don’t know. My advice? Atheists need to instead of talking about a rejection of God and the importance of evolution, give people a sense that they too can question life, questions fate and destiny, and still create a viable, happy family. And that vertical meme inheritance, allowing your numerous children to also freely believe what they want, and listening to the facts, needs to also be prioritized. It’s worked for religious families for thousands of years. We need to utilize every memetic tool at our disposal. Or else we will see atheism and free thought disappear, just like that your super awesome shiny gold pog that just landed facedown.

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In the end, all people are ever going to see is the degree.

September 3, 2009

Today at the gym, I actually heard a girl say…

“But are these friends and stuff really important. In the end, all people are ever going to see is the degree.”

I really, really hope that I took this out of context, or I misheard what she really said. But what scares me is that this kind of sentiment is real. I experienced it in undergrad and even though I changed schools for graduate studies, I’m still hearing it.

Can it be that we, the next movers and shakers of the world, are really this focused? I say ‘focused’ because it has the least negative connotation associated with it. I could also say, “are really this closed minded” or “are really this short sighted” or “are really this stupid?” But the thing is, these kids are just that, stupid. They’ve been taught or, after years of being beaten down, learned, that the only way to make it is through hard work. That the joys of life are secondary to the success. That becoming a doctor is the ultimate goal, not happiness. That success will bring happiness.

I think the most important, and sobering, lesson of my life was that we need to teach ourselves how to be happy. If there’s one thing that does not come with a manual, it’s our emotions. Somehow, in the big genetic mess that is our genome, the hardware of life, we code for how our personality will come together. And through positive and negative events in our development, we shape our cells to trigger genes a certain way, a certainly complex way, that ultimately determines our personality. So no one but you can figure out how to make you happy.

But who am I to judge. We all have to make choices. And we all have to live with the choices we make. It’s not my place to impose my will on others and say you should take college for what it is, an extended summer camp where you can learn what you want to learn, see what you want to see, and experience everything and anything that comes along the way.

College is a ramp to your future. That is definitely true. But like all simple machines, you have a choice: to make the ramp short and steep, or make the ramp long and gentle. I say made my choice. I used my ramp to bypass all the steps ahead of me, but I made that ramp as smooth and enjoyable as I could. You only live once, so you’d might as well make it long and lush. And happy.

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The Big Picture

September 1, 2009

I think I’m approaching graduate school with a very different perspective, and coincidentally a very different goal, than my peers. And while the benefits of that are important, I think I need to start taking a few pages from their books.

The major difference I’m facing has a big part to do with what we each individually want from this 5.5 year experience. For a lot of these kids, they want a Ph.D. in biology and the lab experience and the publishing credits to go on and get more lab experience and publishing credits to someday run their own lab. And to a certain extent, that’s what I think I want too. But while not everyone is as certain about all of this as I make it sound, I definitely feel the most lost. The general consensus of people have broad goals, are unsure of what kind of research they want to do, and what lab they want to end up in. And that’s exactly the point of this first year of rotations: to get a taste of everything you might like to see where your passions lie.

But I’m not so sure about research. I decided to apply and go to graduate school because I thought it was the next logical step. I decided I did not want to pursue chemical engineering, so that took out grad school in engineering and going to work in industry from my list of options. I decided a long time ago not to go to med school, so all that left was this second major in biology. And graduate studies in biology was definitely the best choice for me. Nothing makes me happier than getting to talk about science. Nothing makes me happier than learning some new story about how we came to be or what is the world in which we live. Nothing makes me happier than getting to share those stories with others.

So it made sense. Of all my choices, all my decisions, it made sense to go to grad school. But the thing that I’ve noticed since getting here. Not even that. Since meeting people in my interview weekend or randomly chatting with people on facebook. I have a different goal than everyone else. Everyone else wants great rotations and to find themselves in research, find what they like, find their niche. I want great rotations because I want to find myself in science, find out what’s out there, what’s going on in this world, and get to share the stories that I’ve learned. I want to teach what I’m learning, first and foremost.

But while the big picture in my mind is different, I do need to open my eyes wider and see what is going to be best for my career. because like it or not, I’m on a track to becoming a research biologist, and I need to start acting that way. So after a strenuous day, and a lot of meetings, I decided to switch rotations. These first few rotations I need to put my career first and look at the labs I may want to join. Then maybe I can explore the world.